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Biobanks and the Importance of Detailed Phenotyping: a Case Study – the European Glaucoma Society Glaucogene Project

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Biobanks and the Importance of Detailed Phenotyping: a Case Study – the European Glaucoma Society Glaucogene Project Biobanks and the importance of detailed phenotyping: a case study – the European Glaucoma Society GlaucoGENE project Panayiota Founti, Fotis Topouzis, Leonieke van Koolwijk, Carlo Enrico Traverso, Norbert Pfeiffer, Ananth C Viswanathan To cite this version: Panayiota Founti, Fotis Topouzis, Leonieke van Koolwijk, Carlo Enrico Traverso, Norbert Pfeiffer, et al.. Biobanks and the importance of detailed phenotyping: a case study – the European Glaucoma Society GlaucoGENE project. British Journal of Ophthalmology, BMJ Publishing Group, 2009, 93 (5), pp.577-n/a. 10.1136/bjo.2008.156273. hal-00477843 HAL Id: hal-00477843 https://hal.archives-ouvertes.fr/hal-00477843 Submitted on 30 Apr 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Biobanks and the importance of detailed phenotyping: a case study – the European Glaucoma Society GlaucoGENE project Panayiota Founti1, Fotis Topouzis1, Leonieke van Koolwijk2,3, Carlo Enrico Traverso4, Norbert Pfeiffer5, Ananth C. Viswanathan2,6 1. A’ Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece 2. Glaucoma Research Unit, Moorfields Eye Hospital, London, United Kingdom 3. Glaucoma Service, The Rotterdam Eye Hospital, Rotterdam, The Netherlands 4. Centro di Ricerca Clinica e Laboratorio per il Glaucoma e la Cornea, Clinica Oculistica, Di.N.O.G., University of Genoa, Genoa, Italy 5. Department of Ophthalmology, University Eye Hospital, Mainz, Germany 6. Department of Visual Science, Institute of Ophthalmology, London, United Kingdom Corresponding Author: Ananth C. Viswanathan, FRCOphth MD Mailing Address: Glaucoma Research Unit Moorfields Eye Hospital City Road London, EC1V 2PD Tel. Number: +442075662625 Fax Number: +442075662972 e-mail: [email protected] Keywords: biobank, DNA databank, phenotyping, glaucoma Word count: Abstract 188 words, main text 2996 words 1 Abstract Dissecting complex diseases has become an attainable goal through large- scale collaborative projects under the term “biobanks”. However, large sample size alone is no guarantee of a reliable genetic association study and the genetic epidemiology of complex diseases has still many challenges to face. Among these, issues such as genotyping errors and population stratification have been previously highlighted. However, comparatively little attention has been given to accurate phenotyping. Study procedures of existing large-scale biobanks are usually restricted to very basic physical measurements and non-standardised phenotyping, based on routine medical records and health registry systems. Considering that the objective of an association study is to establish genotype-phenotype correlations, it is doubtful how easily this could be achieved in the absence of accurate and reliable phenotype description. The use of non-specific or poorly defined phenotypes may partly explain the limited progress so far in glaucoma complex genetics. In this report we examine the European Glaucoma Society GlaucoGENE project, which is the only large multicentre glaucoma-specific biobank. Unlike previous biorepositories, this initiative focuses on detailed and standardised phenotyping and is expected to become a major resource for future studies on glaucoma. 2 Introduction The major progress in identifying the genetic basis of Mendelian disorders has not been followed by similar achievements in mapping complex diseases, defined as diseases that not exhibit classic Mendelian inheritance attributable to a single gene but are determined by a number of genetic and environmental factors.1 Specifically, there has been a failure of genetic association studies to discover susceptibility loci or replicate initial positive genotype-phenotype correlations in complex diseases.2-12 Inadequate statistical power to detect small and moderate effects was recognised as one of the major limitations.2,3,13-15 The need for large sample sizes has led to numerous large-scale collaborative projects that systematically store biological material linked to clinical and other information. These so-called “biobanks” are designed to create unprecedented opportunities for understanding the pathogenic basis of common diseases and ultimately for implementing genetic findings in clinical practice and public health.9,16,17 On the other hand, they have raised profound ethical issues18-21 and scepticism on whether benefits will outweigh costs.22-24 What remains unquestionable is that the genetic epidemiology of complex diseases has still many challenges to face, mainly in terms of study design and methodology.7-11,22,23,25-30 Among these, we emphasize the importance of detailed and standardised phenotyping, which has not been given the attention it deserves12 and does not seem to have been employed in some large biobanks. Since complex diseases are characterised by large phenotypic variability1, this raises concerns such as how genetic findings derived from such initiatives could be correctly related to the different clinical aspects of a complex disease. With regards to ophthalmic complex diseases, breakthroughs have been already made in mapping age-related macular degeneration (AMD).31-34 The strong effect of a complement factor H variant in AMD (odds ratio >2.45 and population attributable risk up to 50%) was possibly behind the success of these studies, where 3 well-defined criteria for diagnosis were used, although no detailed phenotyping was considered. However, the identification of genetic variants with smaller effects and associations with specific aspects of the phenotype would have possibly required a more detailed phenotypic assessment. This seems to be the case in glaucoma, where genetic findings mostly refer to the minor fraction of cases that follow mendelian rules of inheritance, meaning that the genetic background of the common, non-mendelian forms of glaucoma remains largely unknown.35-37 In 2010 there will be 60.5 million people with glaucoma worldwide, among which 8.4 million will be bilaterally blind; by 2020, these numbers will increase to 79.6 million and 11.2 million respectively.38 On the basis of new opportunities presented in the postgenomic era, the European Glaucoma Society (EGS) GlaucoGENE project has been designed to provide a reliable, extensive and stable resource to enhance research studies in glaucoma genetics. With detailed and standardised phenotyping as one of its basic principles, this project is not only one of the very few phenotype- genotype databases in the field of ophthalmology, but may also be regarded as a pioneer biobank. Biobanks – definitions and classification A “biobank” generally refers to a repository of biological material. In genetic research the term is typically used to describe a biological sample collection from which genetic information can be extracted, matched with clinical and other information. However, several definitions can be found and no international consensus has been reached. “DNA databank”, “DNA bank” and “genetic dataset” are commonly used synonyms of “biobank”. The American National Bioethics Advisory Commission uses the term “DNA bank” to describe a facility that stores extracted DNA or other biological materials for future DNA analysis, which are usually stored with some form of individual 4 identification for later retrieval.39 The Public Population Project in Genomics (P3G), which is a principal international body for the harmonisation of biobanks, sets the additional criterion of large number of samples collected.40 On the other hand, the Swedish Act on Biobanks (2002:297) focuses on the potential of data re-identification rather than the number of samples41. It has been suggested that what differentiates a genetic study from a biobank is that the former focuses on specific genetic hypotheses, while the latter is oriented toward future hypotheses that may not be framed at the outset.42 Based on overall methodology, biobanks may be either disease-specific or non disease-specific43. The term “population-based biobanks” is commonly used to describe the latter category, although subjects are not always randomly selected from the population of reference. Disease-specific biobanks are usually case-control studies recruiting subjects who have developed the disease of interest, as well as healthy individuals. Non disease-specific biobanks are typically cohort studies, where subjects are recruited from the general population to be followed-up over time; depending on study methodology, the recruitment process may involve only healthy individuals or not. However, this is a very crude classification and several study designs have been employed in biobanks so far. Existing biobanks – how are phenotypes assessed? Based on the catalogue of the P3G observatory, over 100 biobanks with a sample size of more than 10,000 subjects have been completed or are currently being conducted.44 In addition there are several collaborative projects or networks, each one involving a number of biobanks, such as the GenomEUtwin45 and the European Prospective Investigation into
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